James Orton, inventor, mineralogist, explorer, and innovative natural historian succeeded Sanborn Tenney as professor of natural history. Tenney, whose views on natural selection had been scrutinized before his appointment (responding, he classified it among the “infidel notions”), resigned to accept a position at Williams College. Although he was publicly neutral about evolution, Orton was a disciple of Charles Darwin, with whom he conducted a lively correspondence. His classes were among the first in America to include Darwin’s work.

On February 9, 1869, Ellen Swallow '70 wrote, "Professor Orton has accepted our invitation to be professor of natural history. Professor [Adrian John] Ebell is giving a course of lectures [illustrated by "magic latern" slides]. I think the President is secretly chafing under the infliction. Dr. Bishop, one of the trustees, was in at the lectures on Friday, but slept comfortably during the hour and will doubtless say it is all right." Georgia Kendrick, ed., "The Early Days of Vassar, Series II," The Vassar Miscellany, February 1, 1899

Professor of natural history and curator of the Natural History Museum, Orton was also an active researcher and an early scholar and advocate of women’s education. His The Andes and the Amazon (1870) was a landmark work, and for many years The Liberal Education of Women: the Demand and the Method: Current Thoughts in America and England (1873), which he edited, remained the most comprehensive study of its subject.

In 1876 his alma mater, Williams College, awarded Orton a doctoral degree on the basis of his work in South America as well as the research he had conducted while teaching at Vassar. Orton died on Lake Titicaca in the Andes on September 25, 1877, probably from complications of injuries sustained during the mutiny of his native escorts.